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Title: NextGen/GENESiPS      
citations:
26727231
description:
Variability in induced pluripotent stem cell (iPSC) lines remains a roadblock for disease modeling and regenerative medicine. Through linear mixed models we have described different sources of gene expression variability from RNA sequencing data in 317 human iPSC lines from 101 individuals. We found that ~50% of genome-wide expression variability is explained by variation across individuals and identified a set of expression quantitative trait loci that contribute to this variation. These analyses coupled with allele specific expression show that iPSCs retain a subject-specific gene expression pattern. Pathway enrichment and key driver analyses, based on predictive causal gene networks, found that Polycomb targets explain a significant part of the non-genetic variability present in iPSCs within and across individuals. These publically available iPSC lines and genetic datasets will be a resource to the scientific community and will open new avenues to reduce variability in iPSCs and improve their utility in disease modeling. SNP array data from individuals included in RNA-seq transcriptome profiling study of human induced pluripotent stem cells to characterize gene expression variation across individuals and within multiple iPSC lines from the same individual. Genotyping was performed on patient blood. Data availability: SNP-genotyping: dbGaP - current study RNA-seq counts: GEO - GSE79636 FASTQ files: SRA - SRP072417
Identifier:
phs001139.v1.p1
accesstypes:
download
enclave
landingpage: http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001139.v1.p1
authentication: simpleLogin
none
authorization:
none
duaIndividual
name:
Insulin Resistance
Pluripotent Stem Cells
affiliations:
Standford University, Stanford, CA, USA
name:
Thomas Quertermous, MD
roles:
Principal Investigators
affiliations:
Icahn School of Medicine at Mount Sinai, New York, NY, USA
name:
Eric Schadt, PhD
roles:
Principal Investigators
affiliations:
National Institutes of Health, Bethesda, MD, USA
name:
U01HL107388
roles:
Funding Source
performedBy:
TitleNameInstitute Principal InvestigatorsThomas Quertermous, MDStandford University, Stanford, CA, USA Principal InvestigatorsEric Schadt, PhDIcahn School of Medicine at Mount Sinai, New York, NY, USA Funding SourceU01HL107388National Institutes of Health, Bethesda, MD, USA
downloadURL: https://dbgap.ncbi.nlm.nih.gov/aa/wga.cgi?page=DUC&view_pdf&stacc=phs001139.v1.p1
Identifier:
phs001139.v1.p1_policy
name:
Data Use Certificate
Identifier:
1
name:
General Research Use (IRB)
alternateIdentifiers:
yes
types:
Case-Control
dateReleased:
06-07-2016
version:
phs001139.v1.p1
dateModified:
09-12-2016
abbreviation:
NHLBI
name:
National Heart, Lung, and Blood Institute DAC
ID:
0
name:
dbGaP